From: Suzanna L. <su...@fr...> - 2002-10-31 06:03:44
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I find fnbeg and fnend completely uninterpretable. fn could stand for anything and would inevitably be confused and misused. Use either of the more intuitive names. My preference is for pos5 and pos3 because position is more neutral than end which may be construed as always being a terminal end rather than just a location. On Wednesday, October 30, 2002, at 06:45 PM, Scott Cain wrote: > I am sending this to the gmod-devel list to get the opinion of the > larger audience. > > I am inclined to agree with Colin about nomenclature, though I do agree > with you about bioperl's normal/incorrect use of boundaries. Before > bioperl came along I did it the way you propose; it caused much > confusion when I changed my schema to correspond to the bioperl way. > Assuming we use Chris' proposed boundary coordinates, I think using > check constraints is a good idea. > > Other opinions? > > Scott > > On Wed, 2002-10-30 at 20:54, Colin Wiel wrote: >> I preferred your suggestion of pos5 and pos3, as well as my suggestion >> of end5 and end3. I don't think a new chado user will figure out that >> fnbeg stands for "feature natural begin" as easily as they would >> figure >> out that pos5 (or end5) is the "position of the 5' end". >> >> Colin >> >>> -----Original Message----- >>> From: gmo...@li... [mailto:gmod-schema- >>> ad...@li...] On Behalf Of Chris Mungall >>> Sent: Wednesday, October 30, 2002 4:46 PM >>> To: gmo...@li... >>> Subject: [Gmod-schema] cvs changes: companalysis module, sequence >> module >>> >>> >>> I have reworked the tables in the computational analysis module; they >> are >>> now a little less generic than before. there is some docs included in >> the >>> .sql - more needed though... >>> >>> the multiple alignment part (eg for clustal results) is still fluid >>> >>> I have also settled on >>> >>> fnbeg >>> fnend >>> >>> for specifying coordinates - feature natural begin, feature natural >> end >>> >>> ie this is the "real" begin and end >>> >>> we should also possibly include a check constraint to make this >> explicit >>> eg >>> >>> fstrand is null OR (fnend - fnbeg) * fstrand >= 0 >>> >>> >>> this is opposed to the normal (erroneous in my opinion) use of >> start/begin >>> end/stop, as used in bioperl, where >>> >>> start <= end >>> >>> ie they actually mean (low, high) >>> >>> how do we feel about check constraints? >>> >>> >>> >>> ------------------------------------------------------- >>> This sf.net email is sponsored by: Influence the future >>> of Java(TM) technology. Join the Java Community >>> Process(SM) (JCP(SM)) program now. >>> http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> >> >> ------------------------------------------------------- >> This sf.net email is sponsored by: Influence the future >> of Java(TM) technology. Join the Java Community >> Process(SM) (JCP(SM)) program now. >> http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> > -- > ----------------------------------------------------------------------- > - > Scott Cain, Ph. D. > ca...@cs... > GMOD Coordinator (http://www.gmod.org/) > 216-392-3087 > Cold Spring Harbor Laboratory > > > > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future > of Java(TM) technology. Join the Java Community > Process(SM) (JCP(SM)) program now. > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel |